The bootloaders for each of the SODAQ variants can be found with the distributed SODAQ board files, and if you have a programmer you can burn it directly from the Arduino IDE. If you want to find the bootloader bin or hex, have a look at the boards.txt file for the variants which can be found in the SODAQ hardware package directory.
Or you can have a look on the SODAQ Github page (note: the selected tag is the most up to date release):
As far as programmers go, the Atmel-ICE is great tool for SAMD and AVR boards. However, it isn't that cheap. Anything that supports SAMD processors over Serial Wire should work fine. Also any programmer which is known to work with the Arduino Zero boards will be good.