When citing material from Early English Books Online (EEBO), it is important to remember to give the publication details of the original print source as well as the electronic version. You can view these in EEBO by clicking on the full record icon (horizontal page) within the list of Search Results, from within image or full text page views, or from a list of Author's Works. Joseph Gibaldi's MLA Handbook for Writers of Research Papers, 5th ed. (New York: The Modern Language Association of America, 1999), deals with citations of online sources in section 4.9.7., pp.195-96. EEBO an online service to which libraries rather than individuals subscribe; for this category, the MLA Handbook specifies the inclusion of the service's name, the library (or other subscribing institution), the date of access, and the URL of the item. Here is an example based on these guidelines:

Spenser, Edmund. The Faerie Queene. London, 1590. Early English Books Online. Cambridge University Library. 13 May 2003 http://gateway.proquest.com/openurl?ctx_ver=Z39.88-2003&res_id=xri:eebo&rft_val_fmt=&rft_id=xri:eebo:image:29269:1.

These citations would appear differently in footnote or endnote references - with commas instead of stops and brackets around the publication details of the source volume. You should consult Appendix B of the MLA Handbook for details.