Not sure what a guarantor fee is but a guarantor is no different than a co-signer in America which lots of young people need. It's slightly different in Japan in that pretty much everyone needs it but as a foreigner with no Japanese credit history whatsoever it didn't seem unreasonable to be required to have a guarantor. Fortunately my company co-signed the first time and a friend's father the second.
Then, there's plenty of apartments with none of those fees. Here's several just around 1 station for as little as $500 a month
http://zero.chintai.net/double/tokyo/ensen/102050012/
There's thousands of other stations all with places to live at similar prices.