What's the best currently available controller for this setup for 6s? I want to be able to waterproof the ESC and not have overheating problems.
I would go with a MGM car/boat controller. The following should do good: TMM 12018-3 Car / Boat EXPERT+, TMM 16018-3 Car / Boat EXPERT+, TMM 22418-3 Car / Boat EXPERT+ or TMM 16024-3 Car / Boat EXPERT+.