Never been through there with an RV, but I have crossed it several times going from LaGuardia to the site I was working. Since the transports are restricted to upper level, I'd assume the same for RVs. I've taken both upper and lower and don't really ever notice a difference. Sometimes uppers even faster because the lower is clogged with commuters who assume it's faster to avoid trucks.
As an alternative, I had several co-workers who were coming in from the Boston area and would take the Tappan Zee bridge to bypass going through the city itself. Depending on the time you're going through it might be a worthwhile reroute.
There's no use crying over spilled milk, unless it's on your keyboard.