Well, they'll both have their pros and cons. Up until very recently, the LQ1 was the most powerful n/a V6 GM had. The downfalls are that due to being DOHC, the powerband is way up at the top, they're quite temperamental about maintenance (i.e. must make sure timing belt is changed every 60k) and some of the repairs are a pain (i.e. alternator calls for 4 book hours, though many people can get it done in under an hour). If you get a '91 - '94 motor, you can keep your OBDI comp and wiring, though you're getting the lesser powerful LQ1. If you go '96 & up, you get the most powerful LQ1, but you'll need all the wiring and computer to change over to OBDII.
The 3400 is much more readily available, and would probably be a lot easier to find one with low mileage since they were used on much newer cars. They're not quite as powerful, but being they're pushrod motors, you'll have a much more immediate torque/response. However, you will need EVERYTHING associated with the wiring and computer, as well as the trans since you'll have to convert everything to OBDII. How well these mount up to the Gen I w-body cradle, I can't say for sure, though a 3100 (basically the same motor) WAS used in the last year of the Gen I Cutlass Supreme, so I'd venture to say it shouldn't be a problem, unless they drastically changed something for one year.
Keeping it OBDI would obviously be a lot easier, but switching over to OBDII would give you worlds more options as far as tuning and modding.