Yes, we ourselves have endured long lines at NYC locations lately. Much better to rent at LGA as a loyalty member and avoid the lines completely. It sucks having to Uber/Lyft out to the airport for pickup, but no wait and much better selection makes it worth it imho. You can always to a one-way back to NYC so you only have to hoof it to the airport one-way.

JFK/EWR is also an option via public transport as well if you want to be more frugal.