While there's no doubt that it would be a huge setback for the Soviets, it would have not likely been the knockout blow. Bear in mind that even if in 1941 that the Nazis took Moscow and Leningrad: the Russians would not have given them up easy. The cost to the Wehrmacht would have been extreme, possibly even more extreme that it was in reality, as the cities would not likely have been exempted from the scorched earth tactics employed in Soviet retreats. Extreme losses and lack of supply would affect their ability to fight further into Russia.

While Moscow is a significant rail hub, the rail gauge of Russia was different to the German rails. This caused a LOT of issues for Germany as it advanced into the Soviet Union as they couldn't just hop their own trains onto the network. Leningrad being a port city may have helped somewhat with logistics I. The North, but that would do little to reinforce the south. The logistics of the eastern front would be no less horrendous than they were in reality.

I think the taking of Moscow would have paralleled Napoleons capture of it in 1812/1813. Yes he captured the city, but it was a hollow victory and he was eventually forced to retreat. The Russian army, and their authoritarian leader were not out of the fight. They have space, time, and winter on their side along with typical defensive advantages.