Honestly, I'd go E46. Even if money weren't a concern. The E46 is going to be better in just about every regard (except probably straight-line performance and arguably interior material quality).
The E46 is a pretty solid car as far as reliability concerns go. I'd give it a slight reliability nod over the E90 despite its age it is probably a more reliable car. The only real concern for these cars is the cooling system which have been known (although not
too common) to fail in early 100k mileage range (more information can be found with a simple search). Adding to that, in my opinion the E46 online community is in my opinion the largest model specific community there is. So finding DIY's if something does indeed go wrong will be quite easy.
Here is more information on the E46:
http://www.bimmerfest.com/wiki/index.php?title=BMW_E46