Probably an equally stupid question, but can your budget stretch to a taxi fare? The last thing I'd want to do after a 15 hour journey is to hump all my luggage from the bus station to a motel - whatever time of day it was.
By the way, the average age in Naples is about 85, so you're probably quite safe at 1am - they'll all have had their cocoa and gone to bed hours ago.
Never saw any gators in downtown Naples, but there were a couple in the undershoot at Marco Island last time I was there.
(We landed long . . .)