Aside from Altera configurators (like USB blaster II), what are the suggested programmer for production?

Having put many FPGA designs into production, I find the most manufacturing friendly route is to have the devices pre-programmed prior to assembly. This obviates the need for any production line programming setup. For Altera/Intel (or even Xilinx) FPGA devices this means sourcing pre-programmed Flash EEPROM devices from a distributor, which is not hard to do. Companies like Arrow, etc are setup to do this (as well as many offshore distributors).

If you go this route than you typically only need FPGA programming equipment at specific rework stations, not on the assembly line. It also saves production line time, as you no longer have the setup and programming time on the production line, or prior to final test and assembly.