The Talmud in Sanhedrin 32b states:
ת"ר צדק צדק תרדף הלך אחר חכמים לישיבה אחר ר' אליעזר ללוד אחר רבן יוחנן בן זכאי לברור חיל אחר רבי יהושע לפקיעין אחר רבן גמליאל ליבנא אחר רבי עקיבא לבני ברק אחר רבי מתיא לרומי אחר רבי חנניא בן תרדיון לסיכני אחר ר' יוסי לציפורי אחר רבי יהודה בן בתירה לנציבין אחר רבי יהושע לגולה אחר רבי לבית שערים אחר חכמים ללשכת הגזית
Our Rabbis taught: justice, justice shalt thou follow,' this means, Follow the scholars to their academies. e.g.. R. Eliezer to Lydda, R. Johanan b. Zakkai to Beror Hail, R. Joshua to Peki'in, Rabban Gamaliel [II] to Jabneh, R. Akiba to Benai Berak, R. Mathia to Rome, R. Hanania b. Teradion to Sikni, R. Jose [b. Halafta] to Sepphoris. R. Judah b. Bathyra to Nisibis, R. Joshua to the Exile, Rabbi to Beth She'arim or the Sages to the chamber of hewn stones. (Soncino translation)
Regarding Benai Berak the footnote in the Soncino translation says:
One of the cities of the tribe of Dan (Josh. XIX, 45) identified with the modern Benai Berak, a flourishing Jewish Colony.
Commenting on this passage, R. Tzvi Hirsch Chajes wrote as follows:
בני ברק היה בחלקו של דן (יהושע י"ט מ"ה) ולוד היתה מהלך יום אחד מירושלים משנה מעשר שני (פ"ה ב') ובחלקו של בנימין (מגילה דף ד ע"א) ועיין רש"י שם ועתה איך יתכן הספור באגדת פסח דר"א ור"ע שהיו מסובין בבני ברק כל אותו הלילה היינו ליל פסח הרי מקומו של ר"א בלוד ור"א בעצמו ס"ל (סוכה כ"ז ע"א) משבח אני את העצלנין שאינן יוצאין מבתיהם ברגל ושם בסוף הסוגיא ספרו שר"א שבת בסוכתו של ר"י בר"א בקסרי מקשה הש"ס דאיך הניח דירתו ברגל ודחוק הש"ס לומר דשבת הואי ראינו דאי אפשר לומר דר' אליעזר יניח ביתו ברגל וקשה א"כ איך הלך בחג המצות לבני ברק וצע"ג
Benei Berak was in the portion of Dan (Joshua 19:45) and Lod was a journey of one day from Jerusalem [as is known from] the Mishnah in Ma'aser Sheni (5:2), and is in the portion of Benjamin (Megillah 4a), and see Rashi there. And now, how is it possible that the story in the Passover Haggadah of R. Eliezer and R. Akiva who were reclining in Benei Berak that entire night, i.e. the night of Passover? Behold R. Eliezer's locale was Lod, and R. Eliezer himself holds (Succah 27a [it's actually 27b]) "I praise the slothful who do not leave their houses on the holiday"! And there at the end of the discussion [the Talmud] tells that R. Eliezer spent Shabbat in the succah of R. Yochanan Ben Ilai in Ceasaria, [and the Talmud asks] how he could leave his dwelling on the holiday. And the Talmud was forced to say that it was Shabbat [and not a holiday]. We [thus] see that it is impossible to say that R. Eliezer would have left on a holiday. And if so, it is difficult – how could he go to Benei Berak on Passover?
R. Reuven Margoliot attempts to answer this question in Margoliot Hayam (Sanhedrin 32b). He says that in his commentary to the Haggadah he noted that the Mishnah (Ma'aser Sheni 5:9) related an incident in which R. Gamliel and the elders were on a boat and R. Gamliel designated the various tithes. This occurred on the day before Passover which is the time of removal for tithes. Therefore, it is possible that they docked in the port of Jaffa on the day before Passover, and Jaffa is opposite Benei Berak as is clear from Joshua 19:45-46. Thus, they did not have time to go to their homes, so they went with R. Akiva to Benei Berak which was the closest:

According to this as well, it would seem that Benei Berak is the same as, or nearby, modern-day Benei Berak.
As an aside, R. Isaac Abarbanel explained in his commentary to the Haggadah that "Benei Berak" is actually referring to the nice furniture that the rabbis reclined on. Some were troubled by this explanation, as Benei Berak is clearly a place mentioned in Joshua. R. Joseph Messas has a responsum (Otzar Hamichtavim 3:1473)where he addresses this, noting that in his version of Abarbanel's commentary to the Haggadah he first states that Benei Berak is a place, and only then as an additional idea says that it could refer to the furniture.