Unless you want to program a conversion tool or change the audio engine NES Maker uses, Famitracker is the only way unless you want to type every single note by hand into a text editor.
The way NES music works is not compatible with most generic music software. (Generated sound vs recorded sound which NES can't replicate practically.) I am aware of three non native trackers that allow creation of NES music in the first place: Famitracker, Musetracker, and Deflemask. Of the three, Famitracker has several freely available ways to get audio made in it into a game. Musetracker has one freely available way that I'm aware of (which isn't the one that's shipped with NES Maker.) Deflemask has none that I'm aware of.
There are several native trackers (actual NES ROMs that allow creation of music): http://www.nes-audio.com/ , and none of them allow exporting of data in an easy way to use for a game (as far as I can recall).