Till now , no SPICE simulator includes a built-in simulator for substrate noise modeling . Some vendors (like Cadence ) released a seperate programs for this task & can provide you a subcircuit description to include it in your simulator (HSPICE or else) , but not to take the whole job.
Some designers , however , force a noise generator on the body (substrate) element of their critical devices & investigate the transfer function for it . Then it treats it as a usual noise ( or frequency response) analysis. This will not give you a very good results indeed , but may be a prime design