Technically speaking, a clipped sine wave output is capable of better phase noise than a cmos or "TTL" output. So if you are buying a very expensive TCXO and trying to make the best PLL possible, that would be the way to go.
In most cases, though, it will not make a difference. If you are using a modern PLL chip, the very first thing the clock sees is a cmos gate, so if the TCXO had better noise floor than that, it will immediately get degraded by that gate. So in that case I would propbably go with a cmos output.
If you were using an analog phase detector, and some fancy low phase noise dividers (like regenerative), then go with sine wave.
It all depends on what phase noise you are trying to achieve.
Rich