There are multiple things making a stroller comfy for the baby, one of it is padding, yes. Some of the most padded, soft strollers would be Joie which have really nice soft seats. Their bassinets, however, are on the simpler side - some of the best carrycot overall are, I would say, at
Other features making the ride comfortable are larger wheels with suspension, a well-made, sturdy but not too hard frame, and also shade/canopy size. Some of the best made of those are at Bugaboo strollers.
In any case, it also depends on what you, as a parent, are imagining. Some are swearing on the retro-style, rocking strollers, others' kids are loving the harder ride on the grass and fall asleep in such cases immediately (my second son was like that). You'll find what you need by trying a few, maybe go in a baby store and check for yourself, as there is no one universal "best" for all kids and all parents.