Each solvent has its advantages and disadvantages. Methanol is less toxic than acetonitrile and so appeals to green chemistry incentives. It is also generally less expensive than acetonitrile. On the other hand, sometimes higher efficiency and better peak shapes can be obtained using acetonitrile, and therefore it is often the go-to solvent for many typical reversed phase analyses. In Aqueous Normal Phase (ANP), only polar aprotic solvents are suitable and therefore acetonitrile will always be the preferred choice in these cases. If pressure is a concern, acetonitrile has the further advantage of being less viscous.

If you substitute methanol for acetonitrile, be sure to increase the water content in your method to compensate for the differing elution strength between the two solvents.