MSG in HD is still in litigation. Verizon wants to carry it but cablevision will not allow it. FCC ruled that Verizon and other cable providers have the right to carry it, but it is currently in the appeals court as cablevision is contesting the ruling.
The answer is real simple. Cablevision has sold MSG HD programming to other cable companies - Time Warner and Comcast. AT&T and Verizon are phone companies who are now in the cable tv business are direct competition to cable. Since cable companies are in certain territorial areas (e.g. Cablevision cannot be in the same town where Comcast is) and can't compete against each other, and FIOS can be in an area where cable is, they refuse to sell the service to the phone companies.
Yes, this is anti-competitive and monopolistic. The FCC has sued Cablevision over this, and the case was heard by the US Court of Appeals in D.C. (docket number 10-1062). The decision has not come down yet.
Thus FIOS cannot purchase the MSG HD service at this point, until the courts force Cablevision to sell it to them.