Unfortunately we don't a lot of information to determine who GON's mother is.... yet. but I believe this is worth reading.
Greed Island was created 2 yrs after GON was born (Greed Island Nen-game has 10 yrs since his creaton, GON being 12 at this time), so the possibilities of GON being conceived through Greed Island are extremely low.
Also GON doesn't belong to the Zoldick family, this because it's would be so un-interesting if KILLUA and GON where brothers / related, if I have learned something about this author is that the thrill and the story line is so rich, that doing something as simple as making them brothers would greatly reduce the story popularity, and no benefit would come of it.
I read someone saying KOMUI was his mother, cmon really? She is a child, plus GING would not be interested in a person willing to suicide over loosing a game of Gungi.
The manga, and I will only refer to the manga which is the real author story line (Old anime has some things wrong, Illumi being a girl is an example and other stuff you can research on the internet). Mito told GON that both their parents are dead (LIE), we already know that GING is alive, chances of GON's mother being alive are very high due to the tape GING recorded, there is no sense on keeping GON's mother information from him if she is dead, this is one of the first indications/clues we should follow.
Also GING recording was going to tell GON about his real mother. It never reads, let me tell you about how she died or how she was, no past tence, it was a simple, let me tell you about your mother (GON stops the tape at this time). This is another clear indication she is alive, 99% to 1% chance.
Also Ging clearly states "they are separated", dont forget that GING also states that Hunters are greedy people willing to leave everything behind in order to achieve their goals, what you are about to read is only theory I deduced of GING's message to GON... Theory: His mother being a hunter and Ging being a hunter himself, had diferent paths to follow, so they got "separated" (don't assume separation as in a couple just because they conceived GON), they both left GON behind (as cruel as it sounds, remember hunters are greedy) in order for them to achieve their goals (couldn't possibly do it with GON on his/her side).
I'm pretty sure that, eventually, GON's mother will make her appearence, his dad already did, and her mother is an even greater mistery than GING, no other clues have been given, there is a reason for this and only the author will know, any other theories will only be specullation unless clues are seen on the manga.
Gon's mother may be the greatest hunt on the whole storyline, keep looking for clues!
