I've seen spaghetti eels and South American puffers kept together in a retailer's aquarium, and the eel seemed to have mastered the art of discretion. Given marine eels and puffers usually get along, I'd guess they'd be fine together.
AMS is absolutely right about spiny eels. There are some species that go into brackish water, but identifying them isn't easy, and they're frankly happier kept in freshwater aquaria. If I were keeping a spiny eel in brackish water, it would be at SG 1.001 to SG 1.003, and alongside gobies, glassfish, halfbeaks, and so on, rather than a puffer. Spiny eels are quite docile and like peaceful aquaria. Lots of plants are crucial if you don't want them to do suicidal leaps from the tank. In fact, if you want them to swim about during the day, I'd consider floating plants mandatory. In short, not a good choice for a pufferfish aquarium.
Cheers,
Neale