According to MacLysaght's Surnames of Ireland, Raftiss would be a different name from Rafferty. Here's what he says about the names:
There were two separate Irish surnames which have often been treated as interchangeable: (i) Ó Raithbheartaigh (modern form Ó Raifeartaigh), from the Irish rath bheartach, meaning "prosperity wielder"; and (ii) Ó Robhartaigh, from the Irish robharta, meaning "full tide", which was originally anglicized as O'Roarty. MacLysaght says that the two names merged as O'Rafferty for the most part as far back as the 15th century, but that the [O']Roarty form is still found in some places in County Donegal, while the O'Rafferty forrm is common in Tyrone and Louth. There is also a separate surname, Ó Reachtabhra (modern form Ó Reachtaire), from the Irish reacht, meaning "decree", which is normally anglicized as O'Raftery. That name is found primarily in County Mayo, although I think the Rafferty and Raftery forms have sometimes gotten confused in places outside Ireland.
The surname Raftiss had a different origin, although its linguistic derivation is similar to that of the name Raftery. The Irish original was Ó Reachtabhair, once again from the Irish word reacht, but it became Raftiss because of the sibilant way that the letter "r" at the end (a "slender 'r' ") was pronounced in Kilkenny in the past (which is where the name originated). The Leinster dialect of Irish which had that pronunciation is now extinct, but the name's pronunciation had taken hold before then.
So, if you know which county was home to your ancestors, you should be able to figure out which of those names they had originally.