There are two aspects to the answer offered by the NY Times. The first addresses the question of lying to the boss for one's own benefit. Here the Ethicist responds that it is unethical and there is no way around this in reality. As you can read in a related question on JVO – noted alongside the question – Jewish ethics clearly would not endorse such a lie. The second question suggested by the response of the Ethicist is that there are occasions when, for pragmatic reasons, there seems to be no way to avoid a lie. While the Ethicist wishes to “contextualize the degree of real damage” and therefore allow the behavior, I would argue that Judaism would not agree.
The Sages taught that truth was the “seal of God,” one of the key names of the Holy One. In Exodus 23:7 we are specifically enjoined to “stay far away from falsehood.” That injunction includes speech, action and hearing. We should not speak falsely, act falsely or listen to falsehoods.
There is allowance for certain “white lies” – exemplified by the story of Sarah laughing at the idea of the aged Abraham fathering her child. God chooses not to pass the full content of Sarah's comment to Abraham in order to keep the peace. Similarly one is advised to praise the beauty of every bride, even if she may not be beautiful in your eyes. Such lies are characterized by the way they keep the peace and allow one to elevate everyone involved.
In this instance you are being paid for your expertise and time. If you are taking time off during the day or otherwise using company time to go job hunting, you are abusing the conditions of your employment. You are depriving your company of either the time or the expertise they are paying for in order to further your own ends.
I appreciate the dilemma – when can you go for a job interview that is not during working hours? It is better, however, to use your time – a personal day – than it is to use your company's time.