We visited the bio bay at Fajardo last week. I was, sadly, underwhelmed by the experience. I can't say I wished we wouldn't have done it but I also can't say I would recommend it to a friend.

We were staying at the Wyndam and it was a 30+ minute trip each way. I would think it would be a hour from San Juan.

If you go, I would recommend an early trip. We were booked for the 9pm trip that didn't leave until 10:15pm, it made for a very long trip.