My 2 cents:
1. Find out who runs the best practices (if possible) .That's also often a sign of the best coach (regardless of W & L's) I'd lean that way first.
2. IF I understood you correctly options #1 & #3 both practice 2x per week. (IF you son's only playing baseball vs. multi sport then I'd lean towards the extra practice vs option 2)
3. I'll go against the grain with letting your son pick... Your his taxi service and we don't know if you've got other kids to haul around. Once he's old enough to drive himself then I'm all for letting him make his own decisions. Don't be afraid to put yourself, siblings, etc first. IF he's truly driven to succeed this choice won't make or break him.
4. The best players on teams often get the most coaching attention. Don't be afraid to pick a lower level team if the coaches are great. Your son might find he get's more detailed coaching on that team vs. the superstar team. However, I wouldn't want my son to be the very best player on his travel ball team because and I think it would help push him to continue to improve.