So... SSW has the "more correct" numbers at the moment? ???
Actually, the listed cost in SSW is wrong, too, and is off in a different way than MegaMek... ???
But SSW has the correct cost if you dig deep into a unit's description. Specifically, select the unit, then choose Tools-->Show Summary (or click Alt+U), and "Total Cost (Dry)" will be the correct cost.
For example, for a SHD-2H Shadow Hawk (55 tons, 1 LRM, 1 SRM, 1 AC5 ammo, 61,500 C-Bill ammo cost):
True cost: 4,444,057 C-Bills
MML Cost: 4,539,382 C-Bills (+95,325, which equals 61500*(1 + 55/100), the unit type/tonnage-adjusted cost of the ammo)
SSW Listed Cost: 4,505,557 C-Bills (+61,500, which is equals the ammo cost without the final unit type/tonnage adjustment)
SSW Dry Cost: 4,444,057 C-Bills (correct)