There is the Esplanade Hotel which i right in Freo.
Rosie O'Grady's is a pub that has accomodation.
If you have a look at the website stayz there are some options of accomodation on there.
Quest Harbour Village
Norfolk Hotel.

I love freo, it is such a laid back place to visit- very artsy and alternative, they have markets and street performers etc. I hope you get a chance to have a look round while you are over here!