I am separated for 5 months,my wife has had affairs from the first month of separation.we have a 2 year old son.she sleeps with these men in the same room while my son lay sleeping.she lives with her mom ,so she goes out knowing her mom will look after him.I see him every Wednesday and second weekend.she has a bad reputation by the men as being very easy.what can I do to get custody of my son.

In my opinion, you will need a good lawyer and you will need to invest some time to get your presentation organized. Check this: Child Custody Battle - Tips for Your Child Custody Battle (http://divorcesupport.about.com/od/divorceadvicepolls/qt/custody_tips.htm)
Invest some time reading about father's rights, as well. Fathers Rights (http://www.themenscenter.com/National/national06.htm)

If you're legally separated and not seeking reconciliation, is that still an affair?

Typically, promiscuity is not grounds for losing custody of one's child. Although if she is in fact bringing men into her bed in the same room as your child, it is inappropriate at the very least. But how do you know that she is bringing men into the same room as your child?