There has been entries of past editions of NaNoRenO that were made in RPG Maker, like Symbiosis.
Also, in this past thread, sakevisual explicitly says it is fine, with the following caveat:
RPG Maker is definitely allowed for this! Definitions of a visual novel are, as always, very subjective, but for a rough rule of thumb, 70% or more of gameplay should be dialogue or text-based narration with the traditional VN format of text box + full screen sprites.