I can highly recommend Abyss Dive Center, also in Marathon.
I've both dived and taken classes with them and I have enjoyed both. The staff (from owner to captain) tend to be long-term employees (or the owner), and are very friendly and helpful.
Not that the boat is the most important thing but I find that having a good one adds to the comfort level. Theirs takes six divers maximum (although they have taken me out plenty of times with just two), and has a covered, dry, comfortable seating area (separate from the tank/benches). There is also a private area near the head for people who would like to change there.
One thing I like is that you set up your first tank of the day on the dock, so you have plenty of time and space to get everything just "so" (which is especially nice if you haven't been diving in a while or are new).
Feel free to PM me if you want to get into more detail.
Blue Sparkle