Looking on the internet deeply has found these results:

The thief came in through the window. is the most popular phrase on the web.

The thief came in from the window. 10 results on the web	The thief came in through the window. 112 results on the web More popular!
Some examples and use cases from the internet:	Some examples and use cases from the internet:
It doesn't look like this phrase is very popular! The search could not find any examples on the internet.	Jul 28, 2015 ... Lucas thinks the thief came in through the window and out through the front door. "That can be very disturbing for people to know that�... It looks like the thief came in through the window. (CK); [S] � [T] The thief ran away and the policeman ran after him. (CK); [S] � [T] The thief ran away in the�... ... is to go into one side of something and come out the other side. The ink went through the paper and made the table wet. The thief came in through the window. The reporter said,�The thief came in through the window.� The reporter said that the thief. had come, have come, has come. in through the window. Brenda says�...

The thief came in from the window.

10 results on the web

The thief came in through the window.

112 results on the web

More popular!

It doesn't look like this phrase is very popular! The search could not find any examples on the internet.

Jul 28, 2015 ... Lucas thinks the thief came in through the window and out through the front door. "That can be very disturbing for people to know that�...
It looks like the thief came in through the window. (CK); [S] � [T] The thief ran away and the policeman ran after him. (CK); [S] � [T] The thief ran away in the�...
... is to go into one side of something and come out the other side. The ink went through the paper and made the table wet. The thief came in through the window.
The reporter said,�The thief came in through the window.� The reporter said that the thief. had come, have come, has come. in through the window. Brenda says�...