There is no honorable way to leave the organization. I really guess it depends on what you mean by "Best way"
If the agenda is to leave the organization with the least amount of backlash and judicial rammifications would be to simply fade away. Stop going out in field service as a start, gradually only attend Sunday meetings, then leave completely.
However lately the organization is cracking down on faders as well even going so far as to treat them as being disfellowshipped.
In my opinion, its always to leave with integrity and truth on your side. Do your research as you are continuing to do. Jwfacts is a great place to compare watchtower doctrine and Biblical doctrine, focus on the inconsistencies within the organization's past, and within their own doctrines. Specifically what the bible says and how it contradicts with Watchtower doctrine.
The lynchpin of the Watchtower is the 607 bce doctrine. The organization stands or falls on this axiom alone. If they are incorrect about 607 being the destruction of Jerusalem, this means the math leading up to 1914 is incorrect, ergo the day of inspection of the Governing Body is also incorrect. Everything depends on that doctrine. The website gives great detail on this. Also there are resources available that show how you can use only the bible and the Insight books to prove the chronology of 598 being the correct date, USING THE WATCHTOWERS OWN LITERATURE!
If the truth is on your side, you can at least leave with dignity knowing you left on your terms, not theirs. Who knows, maybe you might have some witnesses in your congregation who are also questioning but out of fear do not speak up, you may be that voice for them.
Since I have left, I have had the privlege of helping a couple of witnesses from my old congregation leave. They had the courage to actually call me and ask what really happened and not listen to the gossip.
Anyways hope that helps.