Four Democrats crossed the aisle to vote with the GOP.
The legislation, passed 68-31, would fund the department through the end of September.
A House microphone picked up Hoyer calling McCarthy a "coward" Thursday night.
The bill appears to be on track for passage before Friday's deadline at midnight.
Sen. Joe Donnelly will vote to roll back actions from last year.
The Democrat leader said a "clean" bill to fund Homeland Security would pass the House.
Lawmakers will vote on legislation to fund the Department of Homeland Security.
Rep. Bill Flores (R-Texas) said he's heard of schoolchildren being barred from handing out candy canes with Christmas messages.
Senators have scheduled a string of votes Friday to pass a bill.