This is quite the dilemma as each is a highly satisfying sports cars in its own unique ways, but if you know what you want it may not be so bad. There is a 986 and 987 in my family so here is what I have experienced with these models.

986 pros
intake sound
exhaust sound
mid-engine handling balance
suspension compliance combined with superb handling
steering precision
world-class brakes

986 cons
plasticky and cheap interior
reliability--serious engine issues with early model years
parts and service costs
chassis rigidity not as good as S

987 pros
everything good about the 986 and more
much higher quality interior
intake and exhaust notes even sweeter and more inspiring
shifter even more mechanical feeling
styling has 911 and Carerra GT cues
the elusive ride/handling compromise is stunningly resolved
steering precision
world-class brakes
daily driver level of comfort

987 cons
costs nearly twice what a new S costs when nicely optioned!
chasis still not as rigid as S

 

have you considered bmw m coupe/convertible?

 

I love Porsche but didn't particularly care for the boxster - drive both and see which one you like more.
Aside from the driving experience, other deciding factors were:
* reliability and servicing costs
* aftermarket parts/ability to modify