Both great cars, I have owned the 330Ci Conv, sold then ownd a few other cars, now a 2005 M3 Convertible. I rue'd the day I sold my 330, it was such a great all round car, hence getting back in a BMW Conv a few weeks ago.
Two things strike me: the legroom for adults in the 3 series convertible is ok (not great, but not poor), but the headroom is a little cramped. My adult passengers are OK for short hops, say less than 40 miles, but more than that they have complained of feeling a bit claustrophobic. Its not a car you would want to use for taking passengers long distances.
Secondly, you have not stated whether you are going new or used? If new, the current (E46) shape 3 series convertible is soon to cease production, to be replaced by a new convertible, based on the new (not yet launched)3 series coupe, which will have a folding metal roof. My guess is that a new E46 will take a sizeable hit on residual value over the next 12 months, but if you can live with that, it is a fabulous car. I bought my M3 recently (low mileage used, with hefty discount), specifically because it has the canvas roof, the folding tin tops are just not for me looks-wise, I know I will take a hefty residual hit, but its something I can stomach (just about!)
I guess it really comes down to personal preference. It seems obvious,but you don't say whther you have driven both back to back. Take an (extended) test drive in both to see which you prefer, ideally on the same day - its the weather for it!
Nice dilemma to have, BTW!