I've been diving Misawa for the past two years. This summer alone I logged 96 dives. The primary (local) dive locations are located in Mutsu Bay along the Natudomari and Shimokita Peninsula's, and in the Tsugaru Strait along the Tsugaru Peninsula. Lake Towada offers freshwater altitude diving. Assuming you will be working in or around the Air Base or are otherwise under SOFA status, you should be aware that the entire Pacific coastline of the Aomori Prefecture has been placed off-limits to swimmers and divers.
If you will be working on base then the MWR Outdoor Rec office will become your local dive shop. Although I must include certain caveats to that designation. First, they are focused primarily on conducting dive trips. If there is a trip planned, good luck getting air or renting gear if you need it. They do offer dive certifications (PADI OW, they did do one PADI AOW last year for the first time ever) but most new divers limit themselves to only diving when there is a trip planned. Again, if there is a class going on, air is scarce and so is gear. Also, they will not fill your cylinders, and have no mixed gas capabilities (Nitrox, Trimix etc). Last time I checked, they had a total of nine regulator sets available for rental. The gentleman who runs the MWR dive outfit is retired Army and has been here for over 20 years. He used to have a diving location guide online but has since removed it. I was fortunate to download a copy before he took it down. He keeps a close hold on his wealth of knowledge and does not share it with anyone. It is best to dive here with someone who knows the sites. I would be happy to show you around once you get here.
Second, the dive season here is dictated by the MWR dive locker. Generally, they open up in mid-June and close at the end of October. It all really depends on the weather. It snows like crazy here! Water temperatures in June are in the low 50's but reach into the mid 70's by August. I was diving the last week of October and recorded a 74 deg surface temperature. The air temperature at the same time was 51 deg. I dive a 5mm wet-suit all season.
Third, the diving itself is not too exciting during the day. The depth of most dive's hover around 30-45 feet. There are site's where you can hit 100-130 but there is nothing down there to see. Visibility ranges from a few feet on a bad day to 20-30 feet on a good day. Because this prefecture is rural and not densely populated, it gets very dark at night and as such, night diving is a real treat.
If you have any other questions about diving Misawa let me know.
Cheers!