You basically have two major players in Guam, the is MDA and GTDS (Guam Tropical Dive Station). If I'm correct John went into partnership with someone recently thus there have been changes since I last dived with them.
www.gtds.com
The difference is, MDA caters to the locals and military and GTDS cater to tourist and the Japanese.
They both have big 40 pax boats, per my memory. MDA had two big boats. GTDS one big and one small. They both rent space on their boats to the other dive shops. So realistically, if you dive with a different dive shop, you might have a good chance of being on one of thier boats!
This is old information from when I worked in the business a few years ago. Things change and this info needs to be checked out.
Any hoo, have fun. I really miss diving in Guam. Surfer shorts and a rash guard and deep everyday! Now I live in Hawai'i and still miss diving Guam.
Chris