Is it permissible for me to partner with my wife in purchasing an apartment with money she inherited from her father, knowing that the source of this money might be dubious (a restaurant that serves alcohol)?

There is no impediment to the questioner sharing in the apartment by buying half of it or similar, if they both agree to that. If she knows or strongly believes that some of her father's wealth was acquired from selling alcohol, then she should extract the percentage of the unlawful inheritance from her wealth and give it to the poor and needy. If she does not know the amount, she should make an effort to estimate it.