How should I pluralize MSDS?

No less than OSHA uses MSDSs. MSDS's last S is Sheet.

Recommended Format for Material Safety Data Sheets (MSDSs).

This is also how we refer to them in the Emergency Department. Also:

Free access to more than 4.5 million MSDSs available online, brought to you by 3E - msds.com

If it is always used to mean sheets, plural, then I would not pluralize it again. If it normally stands for sheet, then I would pluralize it, in the same way I would pluralize STD's, SAM's, NGO's, etc.

My instinct would be to write MSDSes, following the general principle of attempting to handle initialisms (in which the letters are pronounced) according to their pronunciation, not their written appearance (as with "an MSDS", not "a MSDS").