Since I have done this 3 times in the last few days and had to look it up each time, I will record it here for posterity.
Need to delete a Team Project you created on VisualStudio.com? You can kill it just like you can kill a Team Project on a local TFS instance. Works with Git projects, too.
tfsdeleteproject /collection:https://[myaccount].visualstudio.com/DefaultCollection TeamProjectName