for donphan you need 3 cards, phanpy, donphan and fighting energy.
For toxicroak you need 2 cards toxicroak and psychic energy.
Toxicroak has a built in SSU, donphan doesn't. donphan damages your pokemon, toxicroak doesn't
For Toxicroak you also need Energy gain or a second energy.
You can't surprise with Toxicroak unless you play Gain, and if you do, you play Cyrus as Gain is not searchable without that. Everything in Donphan is searchable and recoverable.
Toxicroak still OHKOs Luxray with Belt, whereas Donphan leaves it with 10hp (can Bat or Belt, though).
Toxicroak needs to come to rebound from KO, whereas you can attack any time with Donphan. You don't need to wait for your Expert Belt Gyarados to get KO'd in order to return OHKO. Donphan damages your bench though, which makes stuff like Sableye or Azelf more Crobatable.
Oh, and Donphan can actually take a hit from SP, whereas Toxicroak should go down from Garchomp+Crobat.
I'd say Donphan has better overall synergy with Gyarados, especially if Warp Energies are played. You just need to tech for Donphan accordingly (ie. play Roseanne's for access to the energy, have something to get Donphan out from the active position when you need to attack with Gyarados). Seems like a good choice on Pluspower/Warp Energy variant. On Crobat/Cyclone variant, you should seriously consider about playing Croak (on a funny side note, you can do the Cyclone trick with Leap Away to reuse Cyclone's effect later).