Too, two, and to

If I wrote "there are three ways to spell to", that would be wrong because there is only one way to spell to. Likewise, there is only one way to spell too and perhaps two ways to spell two (the other being 2).

So, the only way to write that sentence correctly would be to include all three, or write the transcription, [tu].

To flesh out Kosmonaut's answer a little bit, it doesn't make sense to include all three spellings and say that there are three ways to spell those three spellings. Alternative ways to express what you mean include

The word "to" has two homophones: "two" and "too".

and

There are three words that sound like "to".

(If you have an agreed-upon pronunciation notation, like IPA, you could use that. Presumably that is what Kosmonaut's [tu] is.)