I have a 10 month old who has access to a lot of her older sibling's natural toys. Her favorites are plain wooden blocks, some wooden bowls I found in the thrift store, some Holtztiger woodland creatures (those things have seen daily use for YEARS), a kathe kruse doll, and a little piano (not natural but she loves it). She's not yet into the wooden cars, but her sister was at a year old - the ones with the big wooden wheels and no extra parts to come off. She's also not into the stacking cups or stacking rings yet, but I'm sure she'll come around. She had a little bear rattle she likes too, but she's starting to lose interest. She's starting to like the play kitchen food but mostly just mouths them - so it's good they're plain wood. She likes the play silks but only if Daddy is playing peekaboo with her. (Silks are also something we've had around for years now, in daily use.) And she has a Bolga basket that she loves putting her things into and taking them out again. And books! She loves books. You can often find cool things in the wood section of the thrift store that aren't meant to be toys but work anyway. I guess you can't be 100% sure they're non-toxic but for untreated wood you can use your personal comfort level. DD has a vase and mortar and pestle and set of wooden spoons that she loves to play with. They're all made of wood and very sturdy, don't splinter, etc. She plays with them daily.
My 6 year old likes puzzles, Lego, and this year he's getting a Playmobil castle set. You can find them in wood, too... He's also into cars and setting up scenarios with blocks. You could get him a set of unusual shaped wooden blocks. He's also into books and art supplies and outdoor toys. Bilibos are plastic but are really versatile and fun. How about games, like board games? Or a child sized instrument? Mine really wants a guitar (but he's not getting it yet). If he likes to help you cook you could get him a fun shaped cutting board... although I guess that might not have a huge cool factor. :)
I'd say get him a marble run as those are awesome, but the marbles are a choking hazard for baby. Dominoes OTOH usually are too big to choke on even if one or two get lost around the house. And you can set up lots of fun courses with them.