USB is more universal, that is the largest difference for me. You can go anywhere and USB will be available where SD card readers are far less likely. If you are only dealing with your own devices then such is irrelevant. USB is also far cheaper in my experience but that may have changed considering all the portable devices that use SD cards now.
I would expect the data stored on the chips to have longevity equal to or slightly better than that stored on USB thumb drives.My concern, however, is availability of the means to access the data a few years down the road. Chip readers in off-the-shelf computers are of more recent origin than USB ports so may be around a bit longer. Plus there are plenty of chip readers that can plug into various ports on computers and adapters can be cascaded when (not "if") USB ports are no longer standard.
I base this on seeing vast libraries of 2" video tape for which there are precious few VTRs left functional to play them back and copy them to newer formats.
I would not expect SD formats to outlast USB. Virtually everything is USB these days - it will stick around for decades. Every single computer has USB access, every phone charges through USB and essentially every device that has a SD card in it also has a USB connection. This is not true in the reverse. There are also several versions of chips.
USB is not going anywhere. SD cards will likely last a long time as well but they will disappear if a newer, better version cones out.