Weather Station

Nios, and more in general FPGAs, can virtually read any sensor with a digital interface.

If the sensors you found have spi or i2c, then the task is rather easy, at least at hardware level. You only have to write the proper code to extract data from sensors.

Regarding RTC, you probably need an external device, since one usually wants date and time to be preserved when you turn off the equipment or across power faults; FPGA doesn't support a battery backup feature, then you would lose the rtc information.

Look for example Dallas DS1302, DS1306 or similar: besides the RTC function they also provide a small NV memory which can be useful to store some data.