I see your cruise is getting close
I think the answer is yes and no. Not every ship for each run is checked. I think the Port Authority provides some of the services, and as Nole said the local police.
The US Coast Guard also keeps a close eye on the ships. After 9/11 the Coast Guard would actually escort the ships in and out of ports along with the Harbour Master and Tugs.
No worries and Best to you,