I've stayed at both many times (and liked them) so here is a comparison...

the hix 5th avenue is a tiny hotel - the rooms are tiny - it's fine for one, two will be tight - ask for the "01" rooms - those I found to be the largest. Basically there are 5-6 rooms on a floor, elevators are slow as well. But I like the hotel and the staff a lot. One huge positive is that their cable boxes get nearly every channel imaginable if you like to watch tv.

When the hotel first opened, you could pick up a room there for $150ish which was great - much higher now sadly. Location is good on 5th avenue, couple blocks to 5th and 42nd.

the msg property is very large - the manager says it's the largest hix in the chain - the rooms are a pinch larger (some i've stayed in are much larger) - the free breakfast area is a zoo in the morning - not enough space for the amount of rooms.

Location-wise, it's near MSG and 8th ave and penn station for the a/c/e.

For two of you, unless you need the east side, I'd choose the MSG location. Hope that helps - let me know if you need more.