I don't think I've ever played a piece of Yamaha gear I didn't like, and that includes a few basses. Tobias are also very nice, I've got a Deluxe 5 and couldn't be happier. Check them out at www.musicyo.com. And if he's into building stuff, how about the Carvin kit, I've heard very good things about it.
Contrary to the usual "buy him a piece of crap in case he doesn't like it" advice, I'de say get him a decent playable bass or he's guaranteed not to like it. This is especially true with basses, crappy ones normally require high action to avoid fret buzz and can be really hard to play and off-putting for a beginner. Get him a decent one and if it doesn't work out sell it on eBay.
The amp, if we're talking practicing at home, is not so important at this stage. A small Peavey combo will do.
Final word of advice: He will soon ask for a compressor pedal. Trust me, he will. Don't buy him one. Though it may be handy later with a big bass rig and a band to play with, it can easily disguise sloppy technique and you don't want that at this learning stage. Dynamics are very important on bass and you should learn how to control them with your fingers.
Get him the best bass you can afford. If he quits you'll a least recover part of the $.
At $500, a used fender is where I'd start.
Guild Pilot basses can be had around $400.
Mexican Precision or Jazz basses are about that new.
My preference is used american gear. (Sells more easily)
Might find a used Highway 1 P or J at $400.
He can move up from a cheap amp later on.
Have tried the 30W crate. It seemed Ok to start with.
If you try a few basses in stores you'll get some ideas
what he may like for size and weight.
BTW, how old is he? Small hands/arms or large?
A short scale like a mustang or bronco can be pretty good.
My youngest prefered the sound and balance of a long scale.
Plan on half wounds to start--easier on beginners fingers.
Same as for light gage versus medium strings.
Whatever you buy, have it set up by a competent guitar repairman. Or before you buy ask them for any thoughts.
I happened to play a Fender "Sting" bass which is made in Japan at the last trip to the music store. It is a simple design based on the old telecaster bass. But the quaility and build were extraordianry no less for about $579. It had much the same feel of my long departed 67 Precision.
I would think (maybe) pots and pickup change would be all you would need to take it to the top.
I had a Fernandez 5 string bass that was in excellent condition I picked up a few years ago. But...I really wanted him to learn on a 4 string. I spoke to a lot of people and took into consideration all the great feedback I got here and on the LPF.
Man!!! I thought guitar players (6 string variety) were off the wall on equipment. We got NOTHIN' on Bass players. There are some really nice instruments availabled for what I consider a fair price.
Anyway...I bought what I thought I wouldn't get...a Squire. Jonathan is 10 years old and not a big kid. The Squire is light enough for him and the neck seems to suit his hands. The wood is good...and the pickups don't sound bad to me. I've been told the hardware on the Squire's is pretty crappy. That's ok...I'll replace it if it needs replacing. Right now...the thing is setup very well and he's actually kinda diggin' it. He had his first lesson last week and has his second tomorrow. I think I got lucky on the teacher too. I'm lookin' at his stuff and it's pretty solid. He's teaching him to play without a pick. Best bass players I've played with and seen don't use a pick so I can't fault him there. His music theory is solid as well.
The amp I got is a Behringer 30 watt. I like this little amp. I like playing my guitar through it.
I'm primarily a guitarist & am not extremely knowledgeable about basses... but I recently picked up a new Squire Jazz bass for $159.00 shipped, from The Bass Place in Arizona. It's shoreline gold & is quite the looker. For the money, it's tough to go wrong. Seems like a pretty solid instrument to me, and like you say, you can always upgrade parts & pieces as you go along. My only gripe with it is that the neck feels a bit thin.
BTW, I have a few bass students. I do mostly focus on old school fingerstyle playing, but I also have them work out with the pick a bit, in case they ever need it. For the pick stuff, I usually just show them riffs; for example, the Chris Squire lines in the Yes tune "Roundabout". Good luck to your son!
The next step would be to find a good teacher. Even though I only played electric, the one I had at the Faunt School was an upright player and he had insights that most guitarists simply aren't aware of. For example, there's 5-6 different techniques for just plucking the string (not counting slap and pop, bow or picks) and the way you hold down strings isn't the same either. After studying with him, I was surprised at the number of bass players who lacked this sort of solid foundation. So seek out someone whose primary instrument is bass and can demonstrate superior playing ability and you won't go wrong.
Ah, you bring back memories. I wanted a bass when I was 14 (even though I played guitar) because a couple of guitarists much better than me needed a bassist (one was Brian Setzer - no ****) so I wanted to give it a shot. We got the local Buy Lines used stuff newspaper, called up a number, went down to someone's garage, and bought a used Fender with a funky gold sparkle color and warped neck (which several truss rod adjustments over a couple of weeks fixed) for $130. Sold it 30 years later for $5700. It would fetch $10K+ today.