Hi this device CRS226-24G-2S+RM not layer 3? mikrotik does't say in description of this device and which better amd match with ccr 1036-8g-2s+-em?
1 - CRS226-24G-2S+RM
2 - CRS125-24G-1S-2HnD-IN
3 - CRS125-24G-1S-RM

All CRS devices come with fully functional routerOS, so not lacking L3 features. However the CPU power is limited so don't expect you can go overboard with routing and filtering: it is primarily a switch after al.
Compared to the normal RB devices the CRS range comes with additional features L2 in the switching department. See http://wiki.mikrotik.com/wiki/Manual:CRS_features.
CRS226 has more performance and features than the CRS125 so given your list and the match with CCR1046, I'd go with the 226.
However do be advised that there are some very basic features that you might expect from an enterprise grade switch are missing or only implemented at the software level - then limited by CPU power - e.g. STP, LACP and IGMP snooping to name a few.