What are the best commands for Joint Service (Navy)?

Frankly, any experience that worked for us will be different for you when that time comes. Joint is joint, it is more learning how the other services operate. A lot of that requires a bunch of extra learning on your part. I did a Joint Tour at US Central Command and had a blast. The advice I always told JO's, make every job count, and find a way to make each tour fun. Enjoy!

I served in four joint-service organizations, two of which no longer exist, from 1986 to 1991. As a government contractor, I worked with joint organizations throughout the US and around the world planning military exercises.
-United States Readiness Command, MacDill AFB, FL, no longer exists. Most of its force readiness functions transferred to US Northern Command and the Services.
-Joint Deployment Agency, MacDill AFB, FL, which was absorbed into the United States Transportation Command in 1987
-United States Special Operations Command, MacDill AFB, FL
-United States Transportation Command, Scott AFB, IL

My recommendation for you is serving in a unified command that has an operational navy component. That limits your choices to US Pacific Command, US Forces Korea, US European Command, and US Strategic Command because of the boomers. Your expertise in submarine operations will be most valuable in these types of commands. Also, look for a unified command commander who is a Admiral. Location wise, USPACOM in Hawaii is great unless you have a family with kids. USFK assignments are usually 1-year unaccompanied. USEUCOM is a good deal as would be an assignment to its international counterpart, NATO.