I do cryptarch after bounties, because when I turn in bounties I often have upgrades to do that cost glimmer. If I go the cryptarch with max glimmer (25K), then I don't get glimmer for deleting the blue stuff, but if I just knocked myself down a couple thousand with upgrades I can get some back. If I have room under the glimmer cap, I will do Cryptarch first just in case there is something worth equipping for the bounty turn in.