Yes it is safe to put CLR in your toilet tank.
Just make sure you flush the CLR out of the toilet tank a few times after you do use the CLR in the toilet tank to clean it.
You can spray some CLR onto the sides of the toilet tank after emptying the toilet tank of water and allow it to sit for a few minutes.
Then fill the toilet tank back up and flush it a few times to remove rust stains or calcium deposits.
Or you can pour a cup of CLR into the toilet tank directly with the water in it and then allow it to sit for 30 minutes to an hour.
I will put CLR in my own toilet tank every few months to keep calcium from building up in the toilet tank and prevent rust stains.
You can also put some CLR in your toilet bowl as well and allow it to sit in the toilet bowl for 10 to 20 minutes or longer and then use a toilet brush to scrub the toilet.