The color scheme of the individual craft would depend on the ship it was assigned to. The LCM-3 would be considered "deck cargo" for either a transport or attack transport, and so you would need to find out the measure of the "mother" ship in order to determine which color to use on the individual craft.
For example. If the ship it's assigned to was painted in Measure 21 (overall Navy Blue), then the LCM's assigned to it would be also painted Navy Blue. However, if the ship was painted in Measure 22 (graded with Ocean Grey at the cargo deck level), then the LCM's would be in Ocean Grey. So, it's a modelers choice depending on the ship it's assigned to.