The last time I tried Spyder, I think around 2015-2016, it really struggled with large datasets. A lot of pausing and hanging that wouldn't happen at an IPython prompt. Is that better now?
You should give it a try with our new installers for Windows and macOS, which save you the trouble of installing Anaconda: https://github.com/spyder-ide/spyder/releases/tag/v4.2.1