Well, not the best way but applicable... only for study!

I've received PM asking which tool by Satoshi Tomabechi to use. Generally PPSIQS is used.
But don't use RSA Tool for large composite numbers. It's too slow. I have tested RSA Tool vs PPSIQS and PPSIQS is approximately 3 (!) times faster. I tried RSA-255/256 many times and on my machine I get factors for a bit more than one hour. RSA Tool requires ~4-5 hours for the same task. RSA Tool is designed for 'playing' with numbers and keys generation And it's much better to use specialized tools for factoring.
BTW I'm not sure if RSA Tool keys generation scheme is secure