Dwarf Pea Puffers are best in species only tanks, and depending on the size of the tank, should either be kept along or in large number in order to lessen aggression. If the tank is a 5-15 gallon i would say only keep one as I have a dwarf puffer who became quite territorial and killed 2 other puffers by harassing them and not allowing them to eat.
Bumble bee gobies are also best in species only tanks i believe so im not sure about compatibility with a puffer. Ghost shrimp should be relatively safe as long as they are big enough to not be eaten. And Otocinclus are good tank mates i had 2 otos with my puffer and he tolerated them.