I think this would be the best bet. Have the pagan Old Prussians convert to Orthodoxy, and with substantial Russian help beat off the Germans, Danes and Swedes. Orthodox Prussia will fall into the Russian cultural orbit, and Lithuania will follow. IOTL it was substantially within the Russian cultural sphere (if you wanted a book in pagan Lithuania, it was probably written in Russian) until the repeated unions with Poland. If Prussia is Orthodox, Lithuania will most likely go Orthodox as well, and both will be Russian culturally and maybe a bit genetically due to intermarriage with the Russian principalities, since Prussia and Lithuania will be considered the western members of that club. Now Prussia by itself probably doesn't have the strength to unite Russia a la Muscovy, but a Prussia-Lithuania Union could.