We report results of the most sensitive search to date for periodic gravitational waves from Cassiopeia A, Vela Jr., and G347.3 with frequency between 20 and 1500 Hz. The search was made possible by the computing power provided by the volunteers of the Einstein@Home project and improves on previous results by a factor of 2 across the entire frequency range for all targets. We find no significant signal candidate and set the most stringent upper limits to date on the amplitude of gravitational wave signals from the target population, corresponding to sensitivity depths between 54 1/Hz and 83 1/Hz, depending on the target and the frequency range. At the frequency of best strain sensitivity, near 172 Hz, we set 90% confidence upper limits on the gravitational wave intrinsic amplitude of h090%≈10−25, probing ellipticity values for Vela Jr. as low as 3×10−8, assuming a distance of 200 pc.