I know that Khan academy is actively looking for summer interns. Mattermark (YC W13) is also looking for summer interns right now (found in the jobs section of this site).

Another great place to check for internships is angel.co, ventureloop, and also the great HN thread "Who's Hiring April 2014".

Another trick I use to get summer internships is by emailing small companies, (who usually do not have the staff/resources to post on job sites) in the tech industry, and ask them about possible internships. While this approach certainly doesn't work for everyone, the networking/connections you can make are well worth the effort even if you don't land a job.