Home improvement department store like Lowes, Home Depot or Sears. There is a slight difference between the unit you get from local garage door company and the big retailers. The difference is the opener 9ft. rail that allows opener to travel back and forth. The garage door company will install a professional grade opener this means the 9ft. rail is one piece. The retailers sell a rail that comes from factory in pieces so it can fit in a smaller box. The rail that comes in pieces tends to cause problems with opener functions sooner than the openers with a solid rail. Also the pieced rail is not as strong as the solid one.
Home install units tend to have better package deals
These deals may include accessories that you would have to pay extra for with a local garage door co. Like extra remotes, keyless entry and door monitors that let you know if your door is open from inside the home.
Also manufacturer warranties are different on openers sold in hardware stores. A professional grade opener from a garage door company will have a better warranty than one sold at hardware store. This is because units sold at hardware stores are designed for do it yourself installs. When you do it yourself there is the possibility a part of installation can be improper and shorten life of opener. When they are installed by a experienced professional there is far less chance for improper install. Extended warranties from hardware stores can be tricky so read the fine print.