I have figured it out! With help from this site..
http://ebookarchitects.com/conversions/enhanced.php scroll down to the part about XHTML Tables and then 2. Non-Linear XHTML Tables. This method works great. If the table does not fit on a single screen you are able to scroll through it. This site has even posted an example epub file showing this method in action. The table will not be searchable but at least its not getting broken up. I have noticed that in iBooks if a table gets broken up to the next page the borders at the end of the table often get overlapped. (this was while creating the table in InDesign. When I used Dreamweaver to create a table that overflowed to the next page the text often got stacked. It takes a little extra work but I beleive the method shown on the website I linked to is best choice for large tables.