For the most up-to-date basic numbers of nonprofit organizations that file returns and other information about the sector, the National Council of Charitable Statistics is the principal source.

The principal location of data about individual giving and other philanthropy is published by Giving USA Foundation™, a public service initiative of the Giving Institute (formerly the American Association of Fundraising Counsel). The study is researched and written at The Center on Philanthropy at Indiana University. You can reach the website here.

There is a good and up-to-date summary of the essential data describing the nonprofit sector produced by the National Council of Nonprofits 

The main sustained study of the strategic issues that preoccupy nonprofit leaders and managers is The Listening Post Project. This is an initiative  of The Johns Hopkins Center for Civil Society Studies. Up to 750 nonprofits from a range of different subsectors respond to surveys roughly once a quarter.