Using Spacy 2.0.11, you can update its stopwords set using one of the following:

To add a single stopword:

import spacy    
nlp = spacy.load("en")
nlp.Defaults.stop_words.add("my_new_stopword")

To add several stopwords at once:

import spacy    
nlp = spacy.load("en")
nlp.Defaults.stop_words |= {"my_new_stopword1","my_new_stopword2",}

To remove a single stopword:

import spacy    
nlp = spacy.load("en")
nlp.Defaults.stop_words.remove("whatever")

To remove several stopwords at once:

import spacy    
nlp = spacy.load("en")
nlp.Defaults.stop_words -= {"whatever", "whenever"}

Note: To see the current set of stopwords, use:

print(nlp.Defaults.stop_words)

Update : It was noted in the comments that this fix only affects the current execution. To update the model, you can use the methods nlp.to_disk("/path") and nlp.from_disk("/path") (further described at https://spacy.io/usage/saving-loading).