God is actually Sri Krishna and Hindus therefore know him as a male, a He.
It should be recognised that in Hinduism the ‘lingam’ is the symbol of Shiva, the destroyer and procreator in the Trimurti. Shiva is not the Supreme God which is Sri Krishna who appears as a Trimurti of Brahma, Vishnu and Shiva, all of whom are Male. The lingam symbolises the procreation life-generating function of Shiva, whether or not you view it as penis itself that I certainly do.
At a practical level God is creator and preserver and we humans are the created. So he is either a fatherly or a motherly figure to us humans. My experience is that he is a fatherly being rather than a motherly being. One gets to know this when one has established correspondence with God by developing a means of relating to Him such as to be able to see Him responding to you through real life events as the interactions. I have learnt that we humans can go to God as a father figure for knowledge-based guidance and expect stern no-nonsense treatment from Him to our efforts as yogis (gyanyoga, karmayoga and dharmayoga) and intelligence to survive in this world whereas we would only go to our mother for nourishment, love and attention. God is not there to give us personal nourishment, love and attention that is to look after us; in fact He could not care less if we perish due to our own stupidity and laziness. If he was loving us he would make things easy for us and this is not the case as we know from all the human miseries in the world including for people who have worshipped and prayed to God. We have to work hard to survive in this world. If we do so sincerely, truthfully and honestly, whether we are a male or a female, God will assist us by making things happen and with thoughts that will help us to survive and achieve our goals. We then look upon God in awe and to a certain degree fear that comes out of reverence knowing that he is in overall control of our destinies, whereas if God was a motherly figure nurturing us like babies all our lives we would not be having such thoughts. As such God is not a she.
Why is the question of whether God is a male or a female pertinent? If one believes that a Personal God exists to inform us about ourselves as to who we are, how we should lead our lives, and the nature of the world we live in so that we can cope with all the problems that we face through the passage of our lives it is necessary to know whether as children we are dealing with a God as a father figure or a mother figure for we treat these two role-playing differently. Evolutionary biology has made men different from women in the way we look at the world and this gives us our masculine or feminine nature. Women on the whole are more gentle, caring and comforting than men who are more aggressive, ambitious for power (even through violence), and focussed on their major responsibility of looking after the material well being of the family while women are naturally disposed towards child bearing and rearing and looking after the home nest. If one accepts that that there are these fundamental differences between the biology of men and women it is necessary to know who our leader (God) is in these terms when we seek guidance from that figure on how to cope with our lives and cope with our difficulties because we will approach a woman-God with a different attitude than we would a man-God. A neuter gender is not an option in biology of human beings as these are deformities and so we cannot suggest that God is a deformity or a hermaphrodite either. God is also a living being and not a inanimate object to be referred to as ‘it’. So God must have ensured that He would relate to us humans either as a male or as a female. This is why the gender of God is a very relevant question. Since children look up to their father for security as being wiser and more powerful of the two parents in societies with the correct understanding of the natural order (that is in most cultures) and therefore the head of a family, God too is a male figure to whom people should look up to for human well-being generally.
Here is a Biblical/Christian perspective that arrives at the same conclusion in a very interesting manner: http://www.shoutingfromtherooftop.com/god-is-masculine-not-feminine.html
25 January 2014 Update: God is neither a male nor a female. He is without gender for He is a Soul, the Supersoul, the SuperConsciousness. However, at a personal level He can come through to one as either a Male or a Female. In my case that was a Male.