git add . -A
git commit -m "Deleted some files..."
git push origin master
-A Update the index not only where the working tree has a file matching but also where the index already has an entry. This adds, modifies, and removes index entries to match the working tree. Taken from (http://git-scm.com/docs/git-add)
Delete the files from your Explorer view. You see them crossed-out in your Branch view. Then commit and Sync.
Be aware: If files are on your .gitignore list, then the delete "update" will not be pushed and therefore not be visible. VS Code will warn you if this is the case, though. -> Exclude the files/folder from gitignore temporarily.
The easiest thing to do is to move the file from your local directory temporarily, then commit changes to your remote repo. Then add it back to your local repo, make sure to update .gitignore so it doesn't commit to remote again