I drove a 2005 TJ every day for five and a half years (Oct. 16, 2006, until I sold it last summer). It was such an awesome vehicle that I remember the exact date I bought it and have chosen to forget the day I got rid of it.
I just bought an '07 JKU Sahara this weekend. It looks and rides great. The extra room the four-door model provides was one of the main reasons I went with a JK instead of another TJ when I bought another Jeep.
My thoughts: Either vehicle is going to make an awesome platform to build, and both are going to be very capable even if they're bone stock. The JK does ride quite a bit better than the TJ, even with its 3.5 inch lift and 35-inch mud terrain tires. However, some JK owners would have you believe a TJ has the road manners of a farm tractor. That's not the case at all.
Do plenty of research before you jump into something. If you think you're going to keep the Jeep for a while and end up modifying it (as everyone on this forum, including me, seems to do), you're going to want the right platform. What trim is right for you? SE? Sport? X? Sahara? Rubicon? No one on the forum can tell you exactly which one will fit what you think your needs are going to be, but look into the differences in each and decide what's right for you. You'll see differences in the axles, gear ratio, etc., which may or may not be important to you and which you may not have known were even factors when considering what to buy. I know I didn't have a clue when I bought my TJ.
Another option, if you decide you prefer the TJ experience but want a little more room for you and your boy, is an Unlimited TJ (which you'll see referred to as an LJ around here).
Hope this helps.