I did exactly this at Port Canaveral. As it happens I was still back and had myself checked in before my family actually got on the ship, but I did security and the check-in and the KTTW photo by myself after they had already been through. It is POSSIBLE that the system is different in NYC however.
I think one explanation for the differing reports may be that some families arrive together and they ask "Do we all have to go up to the counter, or can hubby stay with the kids while I check us in." The response they get to that question might be, "no you have to all check in together." But what they really mean is that you must all check in, but it doesn't have to be together. The reason all persons must go to the counter is that is when they take the picture that will show up on the CMs monitor every time you hand them your KTTW card. If you are indeed available all at once, they take one group shot and then take it to each KTTW card, but if you go up separately, they can still do it, just with a separately taken picture. Maybe they prefer to do it all at once so it is possible that they say you must all be together to make it easier for them, but there is no technical reason this must be so, especially in the case of the OP who is coming from two different places at two different times. They will almost certainly let you board (and be announced) separately from your spouse and then you can come watch her get announced when she arrives if you like. So long as she is careful not to be LATE.