We used Subway Watersports last year when we were on a cruise ship, as well. We had a good experience; there was a small group of us on the boat, and the dive master was very good. I was a newly certified diver at the time, and this was only my second time on a boat dive (we only did shore dives during my certification course), but he was great - patient and calming.
The only issue that we did have was with our fellow cruise ship passengers, not Subway Watersports. Apparently a family of snorkelers had also made a reservation with Subway, but they arrived at the meeting point 45 minutes late. This meant that we had to wait for them for 45 minutes, and, in turn, the dive boat at the resort that we were going to dive on had to wait for us, so we felt bad for the divers who were actually staying at the resort. Then, when we returned 45 minutes late from our dive (go figure!), the snorkeling woman yelled at us for being late - ha!
Cheers!
Heather W