I can speak for the west coast (not so much for the east coast), but some good schools here are:
In my opinion the two best and likely most competitive are:
Scripps @ UC San Diego (
http://www.sio.ucsd.edu/)
University of Washington (
http://depts.washington.edu/marbio/)
Other top-tier west-coast biology programs with marine faculty are:
UC Santa Barbara (
http://www.msi.ucsb.edu/)
Oregon State University (
http://zoology.science.oregonstate.edu/)
UC Berkley (
http://ib.berkeley.edu/)
Stanford (
http://www.stanford.edu/dept/biology/)
U of Oregon (
http://www.uoregon.edu/~oimb/)
All of that being said, don't be afraid to go to an inland school without a marine biology emphasis. Find a faculty member that is doing work in a marine system you find attractive and shoot to get into that lab. There is a lot of great marine biology going on at schools not known for their marine biology work. Honestly, I think this approach will actually prove to beneficial in the long run. You get a lot of experience marketing your research to non-marine biologists and integrating with them as well. Marine bio programs are crazy competitive, not only for getting in as a grad student, but also gaining a tenure-track faculty position. Having the experience of being a "Marine biologist" at an "Ag school" or something similar, and knowing how to make your skill set and research attractive to those institutions will pay large dividends when trying to get hired soon after getting your Ph.D. or post-doc.
I will spare my whole "why in the world would you want to get your Ph.D. in this day and age; are your crazy?!?!" speech for later....
