Currently, Vishvavani is the only active online Sanskrit magazine. Apoorvavani was the first online Sanskrit magazine but it is currently not active.
Vishvavani is brought out by Campus Samskritam Network (CSN) which mainly consists of members from MIT, UMD, CMU, UPitt, PSU, UPenn, Caltech, Purdue and others. Sowmya Joisa and Avinash Varna are the editors of the magazine.
The group is also promoting Sanskrit blogging and main aim of CSN is to promote Sanskrit, with emphasis on the US and US universities.
Vishvavani is currently hosted on speaksanskrit.org and you can read the magazine for free in PDF format here - Vishvavani Home Page.