With nanoampere signals you really need to take more care with component selection and board layout. Pick physically larger component for increased clearance (E.g. SOIC or DIP instead of TSSOP, 1206 resistors etc). Pull back ground plane further away or maybe don't use ground plane at all around the signals, you don't need it here. Keep voltage gradient between signals uniform and low, don't interleave them. The advice on using [reed] relays are indeed valid here, it's proven good tech when you don't need speed, and the physically larger size helps with signal isolation too. On more extreme case you may need to consider guards and cutouts, but I don't think it's necessary here.
CMOS switch are not generally recommended, usually due to charge injection in addition of potential leakage. In any case it should not be that (1uA) bad. Are you sure they're good parts? Static mishandling for example are good way to blow leakage spec away.