If I were traveling with a child I think I would definitely want more space and a suite. Also, I think the suite hotels are probably more accustomed to meeting the needs of families with children.
The San Carlos and the Affinia 50 are across the street from each other. I haven't been in either one of them, although I walk by them all the time. The Affinia 50 is a 50s/60s building that was probably built as an apartment building. The San Carlos is a pre-war (as in pre WWII) building, more European looking from the outside. If you haven't already done so, you should read the reviews on the site to see how these hotels stack up in terms of your personal preferences. The neighborhood may not be as close to Times Square as you would like, but it is a good central midtown location that isn't all that far from Times Square.
I don't know who owns the San Carlos. The Affinia 50 is owned by a local family company that also owns the Affinia Dumont, the Southgate, Shelburne, Beekman Tower, among others.