Instead of trying to decide between Navy and Marine Corps air, just pick between the Navy and Marine Corps. Look at each service and decide which one offers what you want to experience. Also, talk a look at the career paths beyond just the first flying tour.
The first year for a future Navy pilot vs. a USMC pilot will be much different. If you go the Marine route, you will start out going to The Basic School, and will spend a lot of time doing stuff that has pretty much nothing to do with flying. It's a great way to build quality Marine Officers, but if you want to get in the cockpit right away, it may be something you want to consider.
If you go Navy, you will go right into flight school as soon as you finish OCS. Flight school for Navy and Marine pilots is all the same. Not just the same type of program, the same squadrons, bases, everything. I am Navy, and my on-wing in Primary was a Marine Corps Captain. No sweat. If you go Marine Corps, your first squadron with nothing but Marines will be after you get wings.
The first fleet tour is pretty similar for Navy and Marine pilots. USMC Hornet pilots have a really good chance of deploying on aircraft carriers as just another squadron in the air wing. Navy helo pilots deploy on troop carriers and fly logistic and SAR support with the Marine Air/Ground Task Force that was talked about earlier.
After your fleet tour, things really start to change. I know that Marines can become instructors at flight school, but I really don't know what their other options can be. Navy pilots can be instructors, evaluators at Top Gun or Weapons School (for helo bubbas). Navy types can also serve on an admiral's staff, go to their air wing as a support officer (a non flying job) or go be an NROTC instructor.
Both the Navy and Marines have lots of great options for their pilots. No doubt, each one will have something that you will want to do. Find out the lifestyle that suits you. Blue or green, you can't really go wrong. Both kill the enemy by the thousand so it's all good.