If you can't sort out the buses at Lake Merritt, you can just walk down Oak Street and under the freeway to Jack London Square. I used to work at the BART headquarters there and would walk down there at lunch some days.

I looked at the Waterfont Hotel and they had this info listed:

Downtown Shuttle (FREE)
A free lunchtime shuttle bus connects Jack London Square to downtown Oakland. The shuttle runs along Broadway every six minutes between 11 a.m. and 2 p.m., Monday through Friday.

If you go this route, take a Concord or Richmond train to 12th Street/Oakland City Center.