Larger, older, and more well known than the National Pinto Horse Registry is the Pinto Horse Association, (PtHA). PtHA is a reputable registry. They have been around since the 1930's, they are a larger registry, they require registered bloodlines for all stallions, and they have well organized shows all over the country as well as internationally, with trained/certified judges.
More here-- Welcome to the Pinto Horse Association of America Inc.
If both the sire and dam of your colt were registered as you say, you should probably be able to register him, since both breeds aere on ther approved breeds list. PtHA ? Registration
The only thing I am not 100% sure of is whether the tobiano MFT dam would need to be registered with PtHA first to make the colt eligible. I would contact them and ask.
The above only applies if you want to register him as an intact colt, and/or have his complete pedigree on his PtHA papers. If you geld your colt, then PtHA will register him on his pinto color without regards to pedigree, but if you get all of the paperwork done with his lineage included IMO it would be beneficial even if gelded as it would show his parentage and extended ancestry on his papers then.